title: Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.
abstract: Allosteric signaling within large ribonucleoproteins modulates both catalytic function and biological specificity, but the spatial extent and quantitative magnitudes of long-distance free-energy couplings have yet to be well characterized. Here, we employ pre-steady-state kinetics to generate a comprehensive mapping of intramolecular communication in the glutaminyl-tRNA synthetase:tRNA(Gln) complex. Alanine substitution at 29 positions across the protein-RNA interface reveals distinct coupling amplitudes for glutamine binding and aminoacyl-tRNA formation on the enzyme, respectively, implying the existence of multiple signaling pathways. Structural models suggest that long-range signal propagation from the tRNA anticodon is dynamically driven, whereas shorter pathways are mediated by induced-fit rearrangements. Seven protein contacts with the distal tRNA vertical arm each weaken glutamine binding affinity across distances up to 40 Å, demonstrating that negative allosteric coupling plays a key role in enforcing the selective RNA-amino acid pairing at the heart of the genetic code.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA.
authors.forename: Annia
authors.initials: A
authors.lastname: Rodríguez-Hernández
authors.forename: John J
authors.initials: JJ
authors.lastname: Perona
mesh_terms: D000409:Alanine / Q000235:genetics / Q000378:metabolism; D000494:Allosteric Regulation; D019943:Amino Acid Substitution; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000926:Anticodon; D001665:Binding Sites / Q000235:genetics; D004926:Escherichia coli; D005815:Genetic Code; D005973:Glutamine / Q000378:metabolism*; D006358:Hot Temperature; D007700:Kinetics; D008958:Models, Molecular; D012351:RNA, Transfer, Gln / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction; D013816:Thermodynamics
chemical_list: D000926:Anticodon; D012351:RNA, Transfer, Gln; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; D012261:Ribonucleoproteins; D005973:Glutamine; D000604:Amino Acyl-tRNA Synthetases; C020659:glutaminyl-tRNA synthetase; D000409:Alanine